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Luo J, Huang R, Xiao P, Xu A, Dong Z, Zhang L, Wu R, Qiu Y, Zhu L, Zhang R, Tang L. Construction of hub transcription factor-microRNAs-messenger RNA regulatory network in recurrent implantation failure. J Assist Reprod Genet 2024; 41:3-13. [PMID: 37878219 PMCID: PMC10789703 DOI: 10.1007/s10815-023-02947-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023] Open
Abstract
PURPOSE Recurrent implantation failure (RIF) affects up to 10% of in vitro fertilization (IVF) patients worldwide. However, the pathogenesis of RIF remains unclear. This study was aimed at identifying hub transcription factors (TFs) of RIF in bioinformatics approaches. METHODS The GSE111974 (mRNA), GSE71332 (miRNA), and GSE103465 (mRNA) datasets were downloaded from the Gene Expression Omnibus database from human endometrial tissue using R version 4.2.1 and used to identify differentially expressed TFs (DETFs), differentially expressed miRNAs, and differentially expressed genes for RIF, respectively. DETFs were subjected to functional enrichment analysis and the protein-protein interaction network analysis using the Search Tool for the Retrieval of Interacting Genes (version 11.5) database. Hub TFs were identified using the cytoHubb plug-in, after which a hub TF-miRNA-mRNA network was constructed using Cytoscape v3.8.2. RESULTS Fifty-seven DETFs were identified, in which Gene Ontology analysis revealed to be mainly involved in the regulation of transcription. Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that DETFs were enriched in transcriptional misregulation in cancer, aldosterone synthesis and secretion, AMPK signaling pathway, and cGMP-PKG signaling pathway. EOMES, NKX2-1, and POU5F1 were identified as hub TFs, and a hub TF-miRNA-mRNA regulatory network was constructed using these three hub TFs, four miRNAs, and four genes. CONCLUSION Collectively, we identified three promising molecular biomarkers for the diagnosis of RIF, which may further be potential therapeutic targets. This study provides novel insights into the molecular mechanisms underlying RIF. However, further experiments are required to verify these results.
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Affiliation(s)
- Jiahuan Luo
- Department of Reproductive Genetics, The First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Wuhua District, Kunming, China
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- First Clinical Medical College, Kunming Medical University, Kunming, China
| | - Rongxia Huang
- Department of Gynecology, Kunming Maternal and Child Health Hospital, Kunming, China
| | - Pengying Xiao
- Reproductive Medicine Center, Dongguan Songshan Lake Central Hospital, Dongguan, 523429, China
| | - Anli Xu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Zhaomei Dong
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Lirong Zhang
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Rui Wu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Yunlin Qiu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Li Zhu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China.
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China.
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China.
| | - Ruopeng Zhang
- Reproductive Medicine Center, Dongguan Songshan Lake Central Hospital, Dongguan, 523429, China.
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China.
| | - Li Tang
- Department of Reproductive Genetics, The First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Wuhua District, Kunming, China.
- First Clinical Medical College, Kunming Medical University, Kunming, China.
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Desterke C, Dang J, Lorenzo HK, Candelier JJ. Roles of tetraspanins during trophoblast development: bioinformatics and new perspectives. Cell Tissue Res 2021; 386:157-171. [PMID: 34278518 DOI: 10.1007/s00441-021-03502-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/28/2021] [Indexed: 11/24/2022]
Abstract
Tetraspanins are a superfamily of membrane proteins found in all eukaryotic organisms. They act as scaffold molecules that regulate the traffic and function of other membrane/signaling proteins, resulting in important downstream cellular consequences. The aim of this work was to use transcriptomes and bioinformatics analysis to identify the tetraspanins (and their partners) involved in trophoblast differentiation. We built a protein-protein interaction network around tetraspanins which revealed that tetraspanins CD9, CD81, and CD82 show a specific expression during trophoblast differentiation. These proteins appeared to be interconnected and to recruit several membrane partners which include integrins, immune-related molecules, and a variety of receptors. During weeks 8 to 24, a CD9 expression trajectory was identified in extravillous trophoblasts, and a website was developed: ( https://extravillous.shinyapps.io/CD9humanEVT/ ). In conclusion, CD81 may, together with CD9 and CD82, be interconnected in controlling trophoblast invasion in the endometrium. CD9 expression trajectory in extravillous trophoblast between weeks 8 and 24 shows the involvement of CD9 in cell adhesion and migration.
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Affiliation(s)
- Christophe Desterke
- Université Paris-Saclay, UFR Medicine, Gif-sur-Yvette, France.,INSERM UA9 Hôpital P. Brousse, 14 Avenue P.V. Couturier, 94800, Villejuif, France
| | - Julien Dang
- INSERM U970, 56 rue Leblanc, 75015, Paris, France.,Hôpital Bicêtre, 78 Rue du Général Leclerc, 94270, Le Kremlin-Bicetre, France
| | - Hans-Kristian Lorenzo
- Université Paris-Saclay, UFR Medicine, Gif-sur-Yvette, France.,Hôpital Bicêtre, 78 Rue du Général Leclerc, 94270, Le Kremlin-Bicetre, France.,INSERM U1197, Hôpital P. Brousse, 14 Avenue P.V. Couturier, 94800, Bâtiment Lavoisier, France
| | - Jean-Jacques Candelier
- Université Paris-Saclay, UFR Medicine, Gif-sur-Yvette, France. .,INSERM U1197, Hôpital P. Brousse, 14 Avenue P.V. Couturier, 94800, Bâtiment Lavoisier, France.
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Mid-gestational gene expression profile in placenta and link to pregnancy complications. PLoS One 2012; 7:e49248. [PMID: 23145134 PMCID: PMC3492272 DOI: 10.1371/journal.pone.0049248] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 10/04/2012] [Indexed: 12/25/2022] Open
Abstract
Despite the importance of placenta in mediating rapid physiological changes in pregnancy, data on temporal dynamics of placental gene expression are limited. We completed the first transcriptome profiling of human placental gene expression dynamics (GeneChips, Affymetrix®; ∼47,000 transcripts) from early to mid-gestation (n = 10; gestational weeks 5–18) and report 154 genes with significant transcriptional changes (ANOVA, FDR P<0.1). TaqMan RT-qPCR analysis (n = 43; gestational weeks 5–41) confirmed a significant (ANOVA and t-test, FDR P<0.05) mid-gestational peak of placental gene expression for BMP5, CCNG2, CDH11, FST, GATM, GPR183, ITGBL1, PLAGL1, SLC16A10 and STC1, followed by sharp decrease in mRNA levels at term (t-test, FDR P<0.05). We hypothesized that normal course of late pregnancy may be affected when genes characteristic to mid-gestation placenta remain highly expressed until term, and analyzed their expression in term placentas from normal and complicated pregnancies [preeclampsia (PE), n = 12; gestational diabetes mellitus (GDM), n = 12; small- and large-for-gestational-age newborns (SGA, LGA), n = 12+12]. STC1 (stanniocalcin 1) exhibited increased mRNA levels in all studied complications, with the most significant effect in PE- and SGA-groups (t-test, FDR P<0.05). In post-partum maternal plasma, the highest STC1 hormone levels (ELISA, n = 129) were found in women who had developed PE and delivered a SGA newborn (median 731 vs 418 pg/ml in controls; ANCOVA, P = 0.00048). Significantly higher expression (t-test, FDR P<0.05) of CCNG2 and LYPD6 accompanied with enhanced immunostaining of the protein was detected in placental sections of PE and GDM cases (n = 15). Our study demonstrates the importance of temporal dynamics of placental transcriptional regulation across three trimesters of gestation. Interestingly, many genes with high expression in mid-gestation placenta have also been implicated in adult complex disease, promoting the discussion on the role of placenta in developmental programming. The discovery of elevated maternal plasma STC1 in pregnancy complications warrants further investigations of its potential as a biomarker.
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Rodriguez-Porcel F, Green D, Khatri N, Harris SS, May WL, Lin RCS, Paul IA. Neonatal exposure of rats to antidepressants affects behavioral reactions to novelty and social interactions in a manner analogous to autistic spectrum disorders. Anat Rec (Hoboken) 2011; 294:1726-35. [PMID: 21905242 DOI: 10.1002/ar.21402] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 03/09/2011] [Accepted: 03/10/2011] [Indexed: 11/11/2022]
Abstract
We have demonstrated that neonatal exposure to selective serotonin reuptake inhibitors has lasting effects on behavior and serotonergic neurons in Long Evans rats. Hyperserotoninemia and altered sensory processing are reported in autistic spectrum disorders (ASD). We hypothesized that early life exposure to SSRIs alters sensory processing, disrupts responses to novelty, and impairs social interactions in a manner similar to that observed in ASD. Male and female Long-Evans rat pups were administered citalopram, buproprion, fluoxetine, or saline from postnatal day (P) 8-21. Rats were tested for response to a novel tone before weaning (P25). Later, rats were tested 2× for response to a novel object (P39), and to a novel conspecific (P78, P101). In addition, rats were assessed for juvenile play behaviors (P32-P34) and later, we assessed sexual response to an estrus female in male rats (P153-184). Antidepressant exposure increased freezing after tone, diminished novel object exploration, and reduced conspecific interaction up to 3× compared to saline exposed rats. Juvenile play was profoundly reduced in antidepressant-exposed males when compared to saline exposed groups. Exposure to the SSRIs, but not bupropion disrupted male sexual behaviors. Moreover, specific male responses to female proceptive behaviors were disrupted in SSRI, but not bupropion exposed rats. We conclude that neonatal exposure to antidepressants in rats results in sensory and social abnormalities that parallel many of those reported in ASD.
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Affiliation(s)
- Federico Rodriguez-Porcel
- Department of Psychiatry & Human Behavior, University of Mississippi Medical Center, Jackson, 39216-4505, USA
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